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feat(recom): Add new photodamage function
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The following items are changed:
* the namelists with tuned values (in the respective model setup folder in config)
* Sina's photodamage function
* the possibility to write out grazing of zoo on phyto
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@ogurses
ogurses committed Jun 5, 2024
1 parent caa821e commit 4ef4d5b
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Showing 11 changed files with 738 additions and 330 deletions.
136 changes: 68 additions & 68 deletions config/case_2p1z1d/namelist.recom
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Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@ recom_logfile_outfreq = 2700 !in recom logfile info. output frequency, # s

&pavariables
use_REcoM =.true.
REcoM_restart =.false.
REcoM_restart =.true.

bgc_num = 22 !24 !38 !22
diags3d_num = 28 ! Number of diagnostic 3d tracers to be saved
Expand All @@ -28,10 +28,10 @@ Grazing_detritus = .true.
het_resp_noredfield = .true. ! Decides respiratation of copepod group
diatom_mucus = .true. ! Decides nutrient limitation effect on aggregation
O2dep_remin = .true. ! O2remin Add option for O2 dependency of organic matter remineralization
use_ballasting = .true. ! BALL
use_density_scaling = .true. ! BALL
use_viscosity_scaling = .true. ! BALL
OmegaC_diss = .true. ! DISS Use OmegaC from Mocsy to compute calcite dissolution (after Aumont et al. 2015 and Gehlen et al. 2007)
use_ballasting = .true.
use_density_scaling = .true.
use_viscosity_scaling = .true.
OmegaC_diss = .true. ! Use OmegaC from Mocsy to compute calcite dissolution (after Aumont et al. 2015 and Gehlen et al. 2007) -> set calc_diss_guts to zero if this is false!!!!
CO2lim = .true. ! CO2 dependence of growth and calcification
Diags = .true.
constant_CO2 = .true.
Expand Down Expand Up @@ -80,23 +80,23 @@ recom_Tref = 288.15d0 ! [K]
C2K = 273.15d0 ! Conversion from degrees C to K
Ae = 4500.d0 ! [K] Slope of the linear part of the Arrhenius function
reminSi = 0.02d0
k_o2_remin = 15.d0 ! NEW O2remin mmol m-3; Table 1 in Cram 2018 cites DeVries & Weber 2017 for a range of 0-30 mmol m-3
k_o2_remin = 15.d0 ! O2remin mmol m-3; Table 1 in Cram 2018 cites DeVries & Weber 2017 for a range of 0-30 mmol m-3
/

&palimiter_function
NMinSlope = 50.d0
SiMinSlope = 1000.d0
NCmin = 0.04d0
NCmin_d = 0.04d0
NCmin_c = 0.04d0 ! NEW
NCmin_c = 0.04d0
SiCmin = 0.04d0
k_Fe = 0.04d0
k_Fe_d = 0.12d0
k_Fe_c = 0.09d0 ! NEW
k_Fe_c = 0.09d0
k_si = 4.d0
P_cm = 3.0d0 ! [1/day] Rate of C-specific photosynthesis
P_cm_d = 3.5d0
P_cm_c = 2.8d0 ! NEW
P_cm_c = 2.8d0
/

&palight_calculations
Expand All @@ -107,33 +107,33 @@ a_chl = 0.03d0 ! [1/m * 1/(mg Chl)] Chlorophyll specific at
&paphotosynthesis
alfa = 0.14d0 ! [(mmol C*m2)/(mg Chl*W*day)]
alfa_d = 0.19d0 ! An initial slope of the P-I curve
alfa_c = 0.10d0 ! NEW
alfa_c = 0.10d0
parFrac = 0.43d0
/

&paassimilation
V_cm_fact = 0.7d0 ! scaling factor for temperature dependent maximum of C-specific N-uptake
V_cm_fact_d = 0.7d0
V_cm_fact_c = 0.7d0 ! NEW
V_cm_fact_c = 0.7d0
NMaxSlope = 1000.d0 ! Max slope for limiting function
SiMaxSlope = 1000.d0
NCmax = 0.2d0 ! [mmol N/mmol C] Maximum cell quota of nitrogen (N:C)
NCmax_d = 0.2d0
NCmax_c = 0.15d0 ! NEW
NCmax_c = 0.15d0
SiCmax = 0.8d0
NCuptakeRatio = 0.2d0 ! [mmol N/mmol C] Maximum uptake ratio of N:C
NCUptakeRatio_d = 0.2d0
NCUptakeRatio_c = 0.2d0 ! NEW
NCUptakeRatio_c = 0.2d0
SiCUptakeRatio = 0.2d0
k_din = 0.55d0 ! [mmol N/m3] Half-saturation constant for nitrate uptake
k_din_d = 1.0d0
k_din_c = 0.9d0 ! NEW
k_din_c = 0.9d0
Chl2N_max = 3.15d0 ! [mg CHL/mmol N] Maximum CHL a : N ratio = 0.3 gCHL gN^-1
Chl2N_max_d = 4.2d0
Chl2N_max_c = 3.5d0 ! NEW
Chl2N_max_c = 3.5d0
res_phy = 0.01d0 ! [1/day] Maintenance respiration rate constant
res_phy_d = 0.01d0
res_phy_c = 0.01d0 ! NEW
res_phy_c = 0.01d0
biosynth = 2.33d0 ! [mmol C/mmol N] Cost of biosynthesis
biosynthSi = 0.d0
/
Expand All @@ -144,69 +144,69 @@ ligandStabConst = 100.d0 ! [m3/mumol] order 100. Ligand-free iron sta
/

&pazooplankton
graz_max = 0.31d0 ! [mmol N/(m3 * day)] Maximum grazing loss parameter
epsilonr = 0.09d0 ! [(mmol N)2 /m6] Half saturation constant for grazing loss
res_het = 0.028d0 ! [1/day] Respiration by heterotrophs and mortality (loss to detritus)
graz_max = 2.4d0 ! [mmol N/(m3 * day)] Maximum grazing loss parameter
epsilonr = 0.35d0 ! [(mmol N)2 /m6] Half saturation constant for grazing loss
res_het = 0.01d0 ! [1/day] Respiration by heterotrophs and mortality (loss to detritus)
Redfield = 6.625 ! [mmol C/mmol N] Redfield ratio of C:N = 106:16
loss_het = 0.04d0 ! [1/day] Temperature dependent N degradation of extracellular organic N (EON)
pzDia = 1.0d0 ! Maximum diatom preference
loss_het = 0.05d0 ! [1/day] Temperature dependent N degradation of extracellular organic N (EON)
pzDia = 0.5d0 ! Maximum diatom preference
sDiaNsq = 0.d0
pzPhy = 0.5d0 !1.0d0 ! Maximum nano-phytoplankton preference (NEW: 3/12)
pzPhy = 1.0d0 ! Maximum small phytoplankton preference
sPhyNsq = 0.d0
pzCocco = 0.666d0 ! NEW (8/12)
sCoccoNsq = 0.d0 ! NEW
pzMicZoo = 1.0d0 ! NEW 3Zoo Maximum nano-phytoplankton preference
sMicZooNsq = 0.d0 ! NEW 3Zoo
pzCocco = 0.4d0 ! Maximum coccolithophore preference ! will not be used in the 2p1z1d version
sCoccoNsq = 0.d0
pzMicZoo = 1.0d0 ! Maximum microzooplankton preference ! will not be used in the 2p1z1d version
sMicZooNsq = 0.d0
tiny_het = 1.d-5 ! for more stable computation of HetRespFlux (_plus). Value can be > tiny because HetRespFlux ~ hetC**2.
/

&pasecondzooplankton
&pasecondzooplankton ! will not be used in the 2p1z1d version
graz_max2 = 0.1d0 ! [mmol N/(m3 * day)] Maximum grazing loss parameter
epsilon2 = 0.0144d0 ! [(mmol N)2 /m6] Half saturation constant for grazing loss
res_zoo2 = 0.0107d0 ! [1/day] Respiration by heterotrophs and mortality (loss to detritus)
loss_zoo2 = 0.003d0 ! [1/day] Temperature dependent N degradation of extracellular organic N (EON)
fecal_rate_n = 0.104d0 ! [1/day] Temperature dependent N degradation of \
fecal_rate_c = 0.236d0
fecal_rate_n_mes = 0.25d0 ! NEW 3Zoo
fecal_rate_c_mes = 0.32d0 ! NEW 3Zoo
pzDia2 = 1.5d0 ! Maximum diatom preference
fecal_rate_n_mes = 0.25d0
fecal_rate_c_mes = 0.32d0
pzDia2 = 1.0d0 ! Maximum diatom preference
sDiaNsq2 = 0.d0
pzPhy2 = 0.5d0 ! Maximum diatom preference
pzPhy2 = 0.08d0 ! Maximum small phytoplankton preference
sPhyNsq2 = 0.d0
pzCocco2 = 0.5d0 ! NEW
sCoccoNsq2 = 0.d0 ! NEW
pzHet = 1.5d0 ! Maximum diatom preference
pzCocco2 = 0.8d0 ! Maximum coccolithophore preference
sCoccoNsq2 = 0.d0
pzHet = 1.5d0 ! Maximum mesozooplankton preference
sHetNsq = 0.d0
pzMicZoo2 = 1.0d0 ! NEW 3Zoo Maximum nano-phytoplankton preference
pzMicZoo2 = 1.0d0 ! Maximum microzooplankton preference
sMicZooNsq2 = 0.d0
t1_zoo2 = 28145.d0 ! Krill temp. function constant1
t2_zoo2 = 272.5d0 ! Krill temp. function constant2
t3_zoo2 = 105234.d0 ! Krill temp. function constant3
t4_zoo2 = 274.15d0 ! Krill temp. function constant3
/

&pathirdzooplankton
graz_max3 = 0.46d0 ! NEW 3Zoo [mmol N/(m3 * day)] Maximum grazing loss parameter
epsilon3 = 0.64d0 ! NEW 3Zoo [(mmol N)2 /m6] Half saturation constant for grazing loss
loss_miczoo = 0.01d0 ! NEW 3Zoo [1/day] Temperature dependent N degradation of extracellular organic N (EON)
res_miczoo = 0.01d0 ! NEW 3Zoo [1/day] Respiration by heterotrophs and mortality (loss to detritus)
pzDia3 = 0.5d0 ! NEW 3Zoo Maximum diatom preference
sDiaNsq3 = 0.d0 ! NEW 3Zoo
pzPhy3 = 1.0d0 ! NEW 3Zoo Maximum nano-phytoplankton preference
sPhyNsq3 = 0.d0 ! NEW 3Zoo
pzCocco3 = 0.d0 ! NEW 3Zoo Maximum coccolithophore preference ! ATTENTION: This value needs to be tuned; I start with zero preference!
sCoccoNsq3 = 0.d0 ! NEW 3Zoo
&pathirdzooplankton ! will not be used in the 2p1z1d version
graz_max3 = 0.46d0 ! [mmol N/(m3 * day)] Maximum grazing loss parameter
epsilon3 = 0.64d0 ! [(mmol N)2 /m6] Half saturation constant for grazing loss
loss_miczoo = 0.01d0 ! [1/day] Temperature dependent N degradation of extracellular organic N (EON)
res_miczoo = 0.01d0 ! [1/day] Respiration by heterotrophs and mortality (loss to detritus)
pzDia3 = 0.04d0 ! Maximum diatom preference
sDiaNsq3 = 0.d0
pzPhy3 = 0.08d0 ! Maximum small phytoplankton preference
sPhyNsq3 = 0.d0
pzCocco3 = 0.8d0 ! Maximum coccolithophore preference
sCoccoNsq3 = 0.d0
/

&pagrazingdetritus
pzDet = 0.5d0 ! Maximum small detritus prefence by first zooplankton
pzDet = 0.5d0 ! Maximum small detritus prefence by first zooplankton
sDetNsq = 0.d0
pzDetZ2 = 0.5d0 ! Maximum large detritus preference by first zooplankton
pzDetZ2 = 0.5d0 ! Maximum large detritus preference by first zooplankton
sDetZ2Nsq = 0.d0
pzDet2 = 0.5d0 ! Maximum small detritus prefence by second zooplankton
sDetNsq2 = 0.d0
pzDetZ22 = 0.5d0 ! Maximum large detritus preference by second zooplankton
sDetZ2Nsq2 = 0.d0
pzDet2 = 0.5d0 ! Maximum small detritus prefence by second zooplankton
sDetNsq2 = 0.d0
pzDetZ22 = 0.5d0 ! Maximum large detritus preference by second zooplankton
sDetZ2Nsq2 = 0.d0
/

&paaggregation
Expand All @@ -225,25 +225,25 @@ rho_C1 = 0.1d0 ! [1/day] Temperature dependent C degradatio
&paphytoplankton_N
lossN = 0.05d0 ! [1/day] Phytoplankton loss of organic N compounds
lossN_d = 0.05d0
lossN_c = 0.05d0 ! NEW
lossN_c = 0.05d0
/

&paphytoplankton_C
lossC = 0.10d0 ! [1/day] Phytoplankton loss of carbon
lossC_d = 0.10d0
lossC_c = 0.10d0 ! NEW
lossC_c = 0.10d0
/

&paphytoplankton_ChlA
deg_Chl = 0.25d0 !0.25d0 ! [1/day]
deg_Chl_d = 0.15d0 !0.15d0
deg_Chl_c = 0.2d0 ! NEW (has been 0.5)
deg_Chl = 0.075 !0.2d0 !0.25d0 ! [1/day]
deg_Chl_d = 0.075 !0.3d0 !0.15d0
deg_Chl_c = 0.075 !0.2d0
/

&padetritus_N
gfin = 0.3d0 ! NEW 3Zoo [] Grazing efficiency (fraction of grazing flux into zooplankton pool)
gfin = 0.3d0 ! [] Grazing efficiency (fraction of grazing flux into zooplankton pool)
grazEff2 = 0.8d0 ! [] Grazing efficiency (fraction of grazing flux into second zooplankton pool)
grazEff3 = 0.8d0 ! NEW 3Zoo [] Grazing efficiency (fraction of grazing flux into microzooplankton pool)
grazEff3 = 0.8d0 ! [] Grazing efficiency (fraction of grazing flux into microzooplankton pool)
reminN = 0.165d0 ! [1/day] Temperature dependent remineralisation rate of detritus
/

Expand All @@ -253,8 +253,8 @@ rho_c2 = 0.1d0 ! [1/day] Temperature dependent C degradatio
/

&paheterotrophs
lossN_z = 0.1d0
lossC_z = 0.1d0
lossN_z = 0.15d0
lossC_z = 0.15d0
/

&paseczooloss
Expand All @@ -263,11 +263,11 @@ lossC_z2 = 0.02d0
/

&pathirdzooloss
lossN_z3 = 0.05d0 ! NEW 3Zoo
lossC_z3 = 0.05d0 ! NEW 3Zoo
lossN_z3 = 0.05d0
lossC_z3 = 0.05d0
/

&paco2lim ! NEW
&paco2lim
Cunits = 976.5625 ! Conversion factor between [mol/m3] (model) and [umol/kg] (function): (1000 * 1000) / 1024
a_co2_phy = 1.162e+00 ! [dimensionless]
a_co2_dia = 1.040e+00 ! [dimensionless]
Expand Down Expand Up @@ -297,11 +297,11 @@ RiverFeConc = 100

&pacalc
calc_prod_ratio = 0.02
calc_diss_guts = 0.0d0
calc_diss_rate = 0.005714 ! 20.d0/3500.d0
calc_diss_guts = 0.5d0 ! set to zero if OmegaC_diss is set to false
calc_diss_rate = 0.005714d0 ! 20.d0/3500.d0
calc_diss_rate2 = 0.005714d0
calc_diss_omegac = 0.197d0 ! NEW DISS Value from Aumont et al. 2015, will be used with OmegaC_diss flag
calc_diss_exp = 1.d0 ! NEW DISS Exponent in the dissolution rate of calcite, will be used with OmegaC_diss flag
calc_diss_omegac = 0.197d0 ! Value from Aumont et al. 2015, is used with OmegaC_diss flag
calc_diss_exp = 1.d0 ! Exponent in the dissolution rate of calcite, is used with OmegaC_diss flag
/

&pabenthos_decay_rate
Expand Down
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